2uzh

Mycobacterium smegmatis 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (IspF)

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE

MYCOBACTERIUM SMEGMATIS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	ZINC ION × 3 CYTIDINE-5'-DIPHOSPHATE × 3 1,2-ETHANEDIOL × 2 GLYCEROL × 3 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE × 1 DI(HYDROXYETHYL)ETHER × 2 ACETATE ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0R559_MYCS2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–165； UniProt 1–163 Author chain B； PDBConstruct 3–165； UniProt 1–163 Author chain C； PDBConstruct 3–165； UniProt 1–163

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2uzh
Deposition date deposition_date	2007-04-27
Structure title title	Mycobacterium smegmatis 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (IspF)
Keywords keywords	ISPF, LYASE, MYCOBACTERIA, COMPLEX WITH CDP, NON-MEVALONATE PATHWAY OF ISOPRENOID BIOSYNTHESIS; LYASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2uzh__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2uzh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2uzh__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	21.79 Å
Rg (electron density)	20.51 Å
Total Rg	21.22 Å
Atom count	3411
Residues	461
Excluded volume	59809 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2uzh__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE
Molecular weight formula_weight	16758.9 kDa
EC 编号 ec_number	4.6.1.12
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	3888

GHMMLPRVGLGTDVHPIEAGRPCRLLCLEFDDADGCAGHSDGDVAAHALCDALLSAAGLGDLGTIFGTDRPQWRGASGADMIRHVRGLVENAGFVIGNATVQVIGNRPKVGPRREEAQQVLSELVGAPVSVSATTTDGLGLTGRGEGLAAIATALVAAEPVGDAK

Source Source

Source organism organism	MYCOBACTERIUM SMEGMATIS
NCBI taxonomy ID ncbi_taxonomy_id	1772
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	CYTIDINE-5'-DIPHOSPHATE
Molecular weight formula_weight	403.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
Molecular weight formula_weight	246.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	272

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	2uzhA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	50 — 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Domain ID domain_id	2uzhB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	50 — 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Domain ID domain_id	2uzhC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	50 — 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

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Unit-cell length a length_a	159.121 Å
Unit-cell length b length_b	159.121 Å
Unit-cell length c length_c	54.160 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	I 4
Space-group number int_tables_number	79
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	51.300 Å
R factor r_factor	0.1650
R_work r_work	0.1630
R_free r_free	0.2060

Mycobacterium smegmatis 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (IspF)

1. Protein Identity and Related Structures Protein Identity & Related Structures

2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2uzh__assembly_1__model_1

2uzh__assembly_1__model_1 | I(q)

2uzh__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Mycobacterium smegmatis 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (IspF)

1. Protein Identity and Related Structures Protein Identity & Related Structures

2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2uzh__assembly_1__model_1

2uzh__assembly_1__model_1 | I(q)

2uzh__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)